Polymorphism of mitochondrial DNA 'S' regions among normal cytoplasms of maize

Variability and uniformity of mitochondrial DNA in populations of putative diploid ancestors of common wheat

By using restriction endonuclease digestion patterns, the degree of intraspecific polymorphism of mitochondrial DNA in four diploid species of wheat and Aegilops, Ae. speltoides, Ae. longissima, Ae. squarrosa, and Triticum monococcum, was assessed. The outbreeding Ae. speltoides was found to possess the highest degree of variability, the mean number of nucleotide substitutions among conspecific individuals being 0.027 substitutions per nucleotide site. A very low degree of mtDNA variation was detected among Ae. longissima accessions, with most of the enzyme-probe combinations exhibiting uniform hybridization patterns. The mean number of substitutions among Ae. longissima individuals was 0.001 substitutions per nucleotide site. The domesticated diploid wheat T. monococcum var. monococcum and its conspecific variant T. monococcum var. boeoticum seem to lack mitochondrial DNA variability altogether. Thus, the restriction fragment pattern can be used as a characteristic identifier of the T. monococcum cytoplasmic genome. Similarly, Ae. squarrosa accessions were found to be genetically uniform. A higher degree of variation among accessions is observed when noncoding sequences are used as probes then when adjacent coding regions are used. Thus, while noncoding regions may contain regulatory functions, they are subject to less stringent functional constraints than protein-coding regions. Intraspecific variation in mitochondrial DNA correlates perfectly with the nuclear variability detected by using protein electrophoretic characters. This correlation indicates that both types of variation are selectively neutral and are affected only by the effective population size.

Mitochondrial DNA polymorphisms of Malawian bean lines: further evidence for two major gene pools

Intraspecific mitochondrial DNA (mtDNA) diversity was determined in 23 Phaseolus vulgaris genotypes, and compared to previously observed variability of morphoagronomic characters and isozyme loci. Twenty of the lines were collected from Malawian landraces; the other three were pure-bred cultivars. The mtDNAs were digested with eight restriction endonucleases, revealing complex banding patterns. Southern hybridization using cosmid clones covering about 200-kb of the genome showed a considerable amount of uniformity of the mtDNA banding patterns. However, five restriction fragment length polymorphisms (RFLPs) were detected, dividing the bean lines into two groups corresponding to the previously known Mesoamerican and Andean gene pools of P. vulgaris. The cultivar "Mecosta" was separated from the rest of the lines by an additional RFLP. At least two out of the six RFLPs are believed to be due to base-pair mutation events. Our results provide the first evidence that the cytoplasms of the two major germ plasm pools of beans are distinct.

In vitro selection for methomyl resistance in CMS-T maize

Many plants resistant to methomyl (Lannate), an insecticide which selectively damages maize with the Texas (T) type of cytoplasmic male sterility (CMS-T), were obtained by in vitro selection and also without selection. The selection procedure used 0.6-0.7mM methomyl and callus from CMS-T versions of several field and sweet corn genotypes (W182BN, Wf9, P39, MDM1, SW1 and hybrids of SW1, IL766A1, IL766A2, and 442 with W182BN-N). Addition of 1 mM methomyl to the regeneration medium greatly reduced recovery of methomyl-sensitive escapes. Resistance was linked with reversion to male fertility and maternally inherited. Most progeny of resistant plants exhibited stable maternally inherited resistance for two generations in field tests. First-generation progeny of seven culture-derived plants segregated for resistance and sensitivity; this suggests that ears of these seven regenerants were cytoplasmically chimeral. Resistance to methomyl was associated with resistance to T toxin from Helminthosporium maydis race T and with changes in mitochondrial physiology. Prolonged culture (14-16 months versus 6-8 months) increased the frequency of resistance among both selected and non-selected regenerants. Little or no resistance was found among regenerants from certain genotypes. Selection with methomyl may be useful for production of improved sweet corn lines and as a source of mitochondrial mutants. This system is also convenient for studies of the effects of nuclear background and of culture and selection systems on the generation of cytoplasmic mutants.

Large double-stranded RNA molecules in Phaseolus vulgaris L. are not associated with cytoplasmic male sterility

Two large double-stranded RNA molecules, 15 and 16 kilobases, were detected in cytoplasmic male sterile (CMS) Phaseolus vulgaris by agarose gel electrophoresis. A number of smaller RNA molecules were observed in 'Sprite', a maintainer line, and recurrent backcrossing of CMS P. vulgarisx'Sprite' resulted in a combined electrophoretic pattern of the two large and numerous small RNA molecules. The large RNA molecules were seed and pollen-transmissible, but were not transmitted by grafting. The RNAs were present in revertant and restored lines derived from CMS-Sprite and therefore were not associated with the cytoplasmic male sterile trait.

Mitochondrial DNA duplication/deletion events and polymorphism of the C group of male sterile maize cytoplasms

Five accessions of members of the C group of male sterile maize cytoplasms (BB, C, ES, PR, and RB) in two nuclear backgrounds (A619 and A632) were examined to elucidate the nature of mitochondrial genome diversity within a related group of cytoplasms. Cosmid and plasmid clones carrying single copy and recombinationally active sequences from N and S cytoplasms of maize were used as probes. Although restriction patterns are quite similar, each of the five could be discriminated by evidence of sequence duplication and recombination, deletion of recombinationally active sequences of N, normal cytoplasm, population of mini-circular DNAs, and by restriction patterns. Each member of the group carried a 1,913 bp minicircular mtDNA, while all entries but RB carried a 1,445 bp minicircular mtDNA. Members of the C group clearly are not molecularly identical; evolution of the group included principal genome reorganization involving sequence duplication/deletion events, apparently independent of the cms trait.

Mitochondrial DNA diversity in the genera of Triticum and Aegilops revealed by southern blot hybridization

Southern blot hybridization of total DNA to defined mitochondrial DNA sequences provides a sensitive assay for mtDNA variation in the genera of Triticum and Aegilops. A clear distinction between cytoplasms of tetraploid species sharing the "AG" haploid genome is reported for the first time. The Sitopsis section of the genus Aegilops showed the most extensive intra- and inter-specific variation, whereas no variation could be detected among the cytoplasms of polyploid Triticum species (wheats) sharing the AB haploid genome. Extensive cytoplasmic intraspecific diversity was revealed in Ae. speltoides.

Cloning and characterization of a linear 2.3 kb mitochondrial plasmid of maize

A linear 2.3 kb DNA molecule found in maize mitochondria was cloned into pUC8. A natural deletion of this plasmid, found in cmsT and some N (fertile) types of maize plants, was mapped to one end of the plasmid. A minor sequence homology to S-2, another linear mitochondrial plasmid, was detected, as well as more significant sequence homology with chloroplast and maize nuclear DNA. Hybridization to teosinte mitochondrial DNA (mtDNA) revealed the presence of part of the maize plasmid in the high molecular weight mtDNA of the maize relatives. RNA dot hybridization indicates that the plasmid is transcribed in mitochondria. The termini of the 2.3 kb linear plasmid contain inverted repeated sequences; of the first 17 nucleotides of the termini, 16 are identical to the terminal inverted repeats of the linear S plasmids found in the mitochondria of cmsS maize plants.

A physical map of the sorghum chloroplast genome

The chloroplast genome of the IS1112C cytoplasm of sorghum was mapped by the construction of a Bam-HI library in pUC8, and hybridization with BamHI, SalI, and PstI digests of chloroplast DNA (ctDNA) of sorghum and maize. The molecules are extensively colinear, with only one of 13 SalI fragments differing slightly from maize. Seven of 70 restriction sites differed in the two species. A total molecular size of ca. 138 kb was estimated for sorghum. The inverted repeat was not conserved between sorghum and maize, as revealed by a slightly larger BamHI 16S rDNA fragment in sorghum. Homology of a sequence adjacent to the γbcl gene and one end of the inverted repeat was detected. These homologies were also observed in maize, and suggest that the ctDNA genomes of sorghum and maize share small reiterations of sequences of the inverted repeat.

Properties of the linear N1 and N2 plasmid-like DNAs from mitochondria of cytoplasmic male-sterile Sorghum bicolor

The linear N1 and N2 plasmid-like DNAs were recovered from mitochondria of the IS1112C line of cytoplasmic male-sterile (CMS) Sorghum bicolor (S. bicolor). Molecular clones containing internal sequences of these plasmids were constructed. These clones were used to probe Southern blots of mitochondrial genomes from six CMS and five male-fertile (MF) lines of S. bicolor, as well as Southern blots of IS1112C chloroplast, IS1112C nuclear and kafir nuclear genomes. We found no evidence for integrated copies of N1 or N2 in any of the mitochondrial, chloroplast or nuclear genomes probed in this study. Our clones did detect an N1-homologous transcript of 3.1 kb and N2-homologous transcripts of 3.9 and 1.4 kb in IS1112C mitochondrial RNA prepared from lines with and without nuclear, fertility-restoring genes.N1 and N2 DNAs were degraded by exonuclease III but were resistant to lambda exonuclease, presumably due to the presence of 5' terminal proteins. We detected multimeric forms of N1 and N2 in Southern blots of unrestricted, IS1112C mitochondrial DNA (mtDNA). These forms apparently also had associated protein molecules.

A new source of cytoplasmic male sterility in maize induced by the nuclear gene, iojap

Cytoplasmic male sterility (cms) was found in plants derived from the F2 progeny of fertile, normal cytoplasm plants of the inbred R181 pollinated with a genetic stock carrying the recessive nuclear gene, iojap. The male sterile plants were maintained by back-crossing with the inbred W182BN which maintains all known sources of cytoplasmic male sterility. The new male sterile progeny were found to exhibit stable male sterility under field conditions in two environments. However, they were partially fertile in the hot, dry summer of 1983 at Aurora, NY. It was found that these lines were restored by lines that characteristically restore cms S group cytoplasms. Pollen phenotype studies indicated that the restoration was gametophytic in nature, also characteristic of the cms S group. Agarose gel electrophoresis of undigested mitochondrial DNA (mtDNA) from these steriles indicated that these lines have the S-1 and S-2 episomes characteristic of the cms S group. Restriction endonuclease digest patterns of mtDNA from these sterile lines digested with BamH I indicated that these steriles fit into the CA subgroup of the cms S group. The new source of cms has been designated cms Ij-1.

Fertility restoration and mitochondrial nucleic acids distinguish at least five subgroups among cms-S cytoplasms of maize (Zea mays L.)

Differences in fertility restoration and mitochondrial nucleic acids permitted division of 25 accessions of S-type male sterile cytoplasm (cms-S) of maize into five subgroups: B/D, CA, LBN, ME, and S(USDA). S cytoplasm itself (USDA cytoplasm) was surprisingly not representative of cms-S, since only two other accessions, TC and I, matched its mitochondrial DNA pattern. CA was the predominant subgroup, containing 18 of the 25 accessions. The B/D and ME subgroups were the most fertile and LBN the most sterile. The exceptional sterility of LBN cytoplasm makes it the most promising of the 25 cms-S accessions for the production of hybrid seed. The most efficient means of quantifying the fertility of the subgroups was analysis of pollen morphology in plants having cms-S cytoplasm and simultaneously being heterozygous for nuclear restorer-of-fertility (Rf) genes. This method took advantage of the gametophytic nature of cms-S restoration. The inbred NY821LERf was found to contain at least two restorer genes for cms-S. Fertility differences were correlated with mitochondrial nucleic acid variation in the LBN, ME, and S (USDA) subgroups.

Circular plasmid DNAs from mitochondria of Sorghum bicolor

Agarose gel electrophoresis of mitochondrial DNA (mtDNA) from the IS1112C male-sterile cytoplasm of Sorghum bicolor (S. bicolor) revealed plasmid-like DNAs additional to the linear N1 and N2 molecules. Mitochondrial plasmids were separated from the principal mitochondrial genome and used in the construction of molecular clones. Clones with EcoRI inserts of 1.7 and 2.3 kb were recovered. Hybridization of these clones to Southern blots of unrestricted and EcoRI-digested IS1112C mitochondrial plasmids indicated the cloned inserts were complete or nearly-complete copies of minicircular DNA molecules. These clones were used to probe Southern blots of mitochondrial genomes from six cytoplasmic male-sterile (CMS) and five male-fertile (MF) lines of S. bicolor, as well as Southern blots of IS1112C chloroplast, kafir chloroplast, IS1112C nuclear, and kafir nuclear genomes. The 2.3 and 1.7 kb plasmids had a very limited distribution among the sorghum entries we examined. We found no evidence for integrated copies of these sequences in any of the mitochondrial, chloroplast, or nuclear genomes probed in this study. However, the 2.3 kb sorghum minicircle did hybridize to the 1.94 kb minicircle from maize mitochondria. Hybridization of the 1.7 and 2.3 kb clones to IS111L2C mitochondrial RNA reveal a transcript of 1.1 kb from the 1.7 kb minicircle and transcripts of 1.9 and 1.4 kb from the 2.3 kb molecule.

Molecular analysis of the inheritance and stability of the mitochondrial genome of an inbred line of maize

We have investigated the inheritance of the mitochondrial DNA (mtDNA) restriction endonuclease digestion patterns of maize inbred line B37N in individual plants and pooled siblings in lineages derived from five separate plants in the third generation following successive self-pollinations. The restriction fragment patterns of the different mtDNA samples were compared after digestion with five endonucleases. No differences were visible in the mobilities of the 199 fragments scored per sample. Hybridization analysis with two different cloned mtDNA probes, one of which contains homologies to a portion of the S2 plasmid characteristic of cms-S maize, failed to reveal cryptic variation. The apparent rate of genomic change in maize mtDNA from inbred plants appears to be very slow, compared with the faster rates of change seen in maize tissue cultures and with the documented rapid rate of inter- and intraspecific variation for mammalian mtDNA.

A variant mitochondrial DNA arrangement specific toPetunia stable sterile somatic hybrids

We have characterized two related regions of twoPetunia mitochondrial genomes in order to understand how plant mt genomes from a cytoplasmic male sterile (cms) line and a fertile line diverge from one another. Restriction maps of these regions indicate that a sequence arrangement shared by the two genomes adjoins sequences which are not shared at the corresponding locations in the two genomes. A point where the mt genomes from the cms line and the fertile lines diverge from each other was identified and mapped.Previously we had observed that somatic hybrids constructed from the cms and the fertile line contained mt genomes carrying new combinations of parental mtDNA restriction fragments (3). Using the restriction maps of the two related mtDNA regions, a mtDNA arrangement unique to the cms parent could be shown to be present in all 17 stable sterile somatic hybrids tested and none of the 24 stable fertile somatic hybrids tested. This data does not exclude the possibility that additional, as yet unidentified, mtDNA arrangements unique to the cms parent might also be found exclusively in sterile somatic hybrids. Whether or not the sterile parental mtDNA arrangement reported here is functionally related to cms, it apparently segregates with cms in somatic hybrids.

Variable presence of the 1.94kb mitochondrial plasmid in maize S cytoplasm and its relationship to cytoplasmic male sterility

Mitochondrial DNA (mtDNA) was isolated from over 100 different maize nucleo-cytoplasmic combinations. DNA preparations were assayed for the presence of the 1.94kb mitochondrial plasmid by agarose gel electrophoresis and hybridization to a recombinant clone of the plasmid. The plasmid was present in all tested inbreds which carried N, male fertile, cytoplasm or the cytoplasmically male sterile (cms) groups,cms-T andcms-C. However, members of thecms-S group differed with respect to the presence of the plasmid. Cytoplasms I, J and S possessed the plasmid, whereas cytoplasms B, CA, D, G, H, IA, ME, ML, PS, RD and VG did not.Cms-S group lines which had spontaneously reverted to fertility (nuclear and cytoplasmic revertants) did not exhibit a concomitant change in 1.94kb plasmid levels, although all such lines showed the previously reported alteration in levels of the linear mtDNAs, S1 and S2. The presence or absence of the plasmid was not correlated with (i) frequency of reversion to fertility, (ii) the degree of male sterility expressed, (iii) the presence or absence of standard nuclear restorer to fertility genes and (iv) nuclear genotype. Latin American races carrying RU cytoplasm possessed the plasmid, as did sweet corn varieties. The relevance of the data tocms and evolution of thecms-S group is discussed.

Homology between the ribosomal DNA of Escherichia coli and mitochondrial DNA preparations of maize is principally to sequences other than mitochondrial rRNA genes

E. coli ribosomal DNA has been used to probe maize mitochondrial DNA. It hybridizes primarily with chloroplast ribosomal DNA sequences and with fungal and bacterial sequences which may contaminate the mtDNA preparations. It also hybridizes to the chloroplast 16S ribosomal RNA gene sequence present in the mitochondrial genome (1) as well as to the mitochondrial 18S ribosomal RNA gene sequence. Weak sequence homology was detected between E. coli rDNA and the mitochondrial 26S ribosomal RNA gene.

Molecular analysis of genomic stability of mitochondrial DNA in tissue cultured cells of maize

Mitochondrial DNA (mtDNA) of the Black Mexican sweet line of maize isolated from tissue cultured cell suspension cultures and young seedlings was examined. Restriction fragments generated by two endonucleases were comparatively analyzed by visualization of ethidium bromide stained gels as well as by membrane hybridization with nick-translated DNA probes of plasmid-like S1 and S2 DNA. Although no major molecular alterations were seen in tissue cultured cells, the samples were clearly not identical. The variation was mainly in the stoichiometry of several restriction fragments. Hybridization analyses with S1 and S2 probes show no evidence of molecular rearrangement in this part of the genome in tissue cultured cells. Minor variations in restriction patterns could reflect alterations in frequency of circular mtDNA molecules, perhaps related to nuclear alterations during the extended period of culture.